scPDB - 5f5r entry

Protein Data Bank Entry:

PDB ID : 5f5r

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2015-12-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Heat shock protein 75 kDa, mitochondrial
ID:	TRAP1_HUMAN
AC:	Q12931
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	16.193
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.604	489.375

% Hydrophobic	% Polar
41.38	58.62
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	47.78 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-41.4674	58.0173	72.9789

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O2A	ND2	ASN- 119	2.83	137.53	H-Bond (Protein Donor)	false
N6	OD1	ASP- 158	2.8	166.78	H-Bond (Ligand Donor)	false
C1'	SD	MET- 163	4.04	0	Hydrophobic	false
C4'	CB	ASN- 171	4.06	0	Hydrophobic	false
C1'	CB	ASN- 171	3.74	0	Hydrophobic	false
C1'	CD2	LEU- 172	4.35	0	Hydrophobic	false
O2G	CZ	ARG- 177	3.76	0	Ionic (Protein Cationic)	false
O1A	N	PHE- 205	2.86	175.05	H-Bond (Protein Donor)	false
O1G	MG	MG- 301	2.02	0	Metal Acceptor	false
O1B	MG	MG- 301	2.06	0	Metal Acceptor	false
O2A	MG	MG- 301	2.01	0	Metal Acceptor	false
N1	O	HOH- 429	2.72	149.84	H-Bond (Protein Donor)	false
O1G	O	HOH- 455	2.77	170.19	H-Bond (Protein Donor)	false